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Barinov NA, Ivanov DA, Dubrovin EV, Klinov DV. Atomic force microscopy investigation of DNA denaturation on a highly oriented pyrolytic graphite surface. Int J Biol Macromol 2024; 267:131630. [PMID: 38631581 DOI: 10.1016/j.ijbiomac.2024.131630] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Revised: 04/06/2024] [Accepted: 04/13/2024] [Indexed: 04/19/2024]
Abstract
Understanding of DNA interaction with carbonaceous surfaces (including graphite, graphene and carbon nanotubes) is important for the development of DNA-based biosensors and other biotechnological devices. Though many issues related to DNA adsorption on graphitic surfaces have been studied, some important aspects of DNA interaction with graphite remain unclear. In this work, we use atomic force microscopy (AFM) equipped with super-sharp cantilevers to analyze the morphology and conformation of relatively long DNA molecule adsorbed on a highly oriented pyrolytic graphite (HOPG) surface. We have revealed the effect of DNA embedding into an organic monolayer of N,N'-(decane-1,10-diyl)-bis(tetraglycinamide) (GM), which may "freeze" DNA conformation on a HOPG surface during drying. The dependence of the mean squared point-to-point distance on the contour length suggests that DNA adsorbs on a bare HOPG by a "kinetic trapping" mechanism. For the first time, we have estimated the unfolded fraction of DNA upon contact with a HOPG surface (24 ± 5 %). The obtained results represent a novel experimental model for investigation of the conformation and morphology of DNA adsorbed on graphitic surfaces and provide with a new insight into DNA interaction with graphite.
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Affiliation(s)
- Nikolay A Barinov
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation
| | - Dmitry A Ivanov
- Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Institut de Sciences des Matériaux de Mulhouse - IS2M, CNRS UMR7361, 15 Jean Starcky, Mulhouse 68057, France
| | - Evgeniy V Dubrovin
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation; Lomonosov Moscow State University, Leninskie Gory 1 bld. 2, 119991 Moscow, Russian Federation.
| | - Dmitry V Klinov
- Moscow Institute of Physics and Technology, Institutskiy Per. 9, Dolgoprudny 141700, Russian Federation; Sirius University of Science and Technology, 1 Olympic Ave, 354340 Sochi, Russian Federation.
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2
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Gao Y, Wang Y. Interplay of graphene-DNA interactions: Unveiling sensing potential of graphene materials. APPLIED PHYSICS REVIEWS 2024; 11:011306. [PMID: 38784221 PMCID: PMC11115426 DOI: 10.1063/5.0171364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
Graphene-based materials and DNA probes/nanostructures have emerged as building blocks for constructing powerful biosensors. Graphene-based materials possess exceptional properties, including two-dimensional atomically flat basal planes for biomolecule binding. DNA probes serve as excellent selective probes, exhibiting specific recognition capabilities toward diverse target analytes. Meanwhile, DNA nanostructures function as placement scaffolds, enabling the precise organization of molecular species at nanoscale and the positioning of complex biomolecular assays. The interplay of DNA probes/nanostructures and graphene-based materials has fostered the creation of intricate hybrid materials with user-defined architectures. This advancement has resulted in significant progress in developing novel biosensors for detecting DNA, RNA, small molecules, and proteins, as well as for DNA sequencing. Consequently, a profound understanding of the interactions between DNA and graphene-based materials is key to developing these biological devices. In this review, we systematically discussed the current comprehension of the interaction between DNA probes and graphene-based materials, and elucidated the latest advancements in DNA probe-graphene-based biosensors. Additionally, we concisely summarized recent research endeavors involving the deposition of DNA nanostructures on graphene-based materials and explored imminent biosensing applications by seamlessly integrating DNA nanostructures with graphene-based materials. Finally, we delineated the primary challenges and provided prospective insights into this rapidly developing field. We envision that this review will aid researchers in understanding the interactions between DNA and graphene-based materials, gaining deeper insight into the biosensing mechanisms of DNA-graphene-based biosensors, and designing novel biosensors for desired applications.
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Affiliation(s)
- Yanjing Gao
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
| | - Yichun Wang
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana 46556, USA
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3
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Panneer Selvam S, Cho S. Phosphate-driven H 2O 2 decomposition on DNA-bound bio-inspired activated carbon-based sensing platform for biological and food samples. Food Chem 2023; 421:136234. [PMID: 37119688 DOI: 10.1016/j.foodchem.2023.136234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/01/2023]
Abstract
Hydrogen peroxide (H2O2) is one of the most important reactive oxygen species (ROS). Increased endogenous H2O2 levels indicate oxidative stress and could be a potential marker of many diseases, including Alzheimer's, cardiovascular diseases, and diabetes. However, consuming H2O2-incorporated food has adverse effects on humans and is a serious health concern. We used salmon testes DNA with bio-inspired activated carbon (AC) as an electrocatalyst for developing a novel H2O2 sensor. The phosphate backbone of DNA contains negatively charged oxygen groups that specifically attract protons from H2O2 reduction. We observed a linearity range of 0.01-250.0 μM in the H2O2 reduction peak current with a detection limit of 2.5 and 45.7 nM for chronoamperometric and differential pulse voltammetric studies. High biocompatibility of the sensor was achieved by the DNA, facilitating endogenous H2O2 detection. Moreover, this non-enzymatic sensor could also help in the rapid screening of H2O2-contaminated foods.
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Affiliation(s)
- Sathish Panneer Selvam
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13210, Korea
| | - Sungbo Cho
- Department of Electronic Engineering, Gachon University, Seongnam-si, Gyeonggi-do 13210, Korea; Gachon Advanced Institute for Health Science & Technology, Gachon University, Incheon 21999, Korea.
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Paloncýová M, Pykal M, Kührová P, Banáš P, Šponer J, Otyepka M. Computer Aided Development of Nucleic Acid Applications in Nanotechnologies. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2022; 18:e2204408. [PMID: 36216589 DOI: 10.1002/smll.202204408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2022] [Revised: 09/12/2022] [Indexed: 06/16/2023]
Abstract
Utilization of nucleic acids (NAs) in nanotechnologies and nanotechnology-related applications is a growing field with broad application potential, ranging from biosensing up to targeted cell delivery. Computer simulations are useful techniques that can aid design and speed up development in this field. This review focuses on computer simulations of hybrid nanomaterials composed of NAs and other components. Current state-of-the-art molecular dynamics simulations, empirical force fields (FFs), and coarse-grained approaches for the description of deoxyribonucleic acid and ribonucleic acid are critically discussed. Challenges in combining biomacromolecular and nanomaterial FFs are emphasized. Recent applications of simulations for modeling NAs and their interactions with nano- and biomaterials are overviewed in the fields of sensing applications, targeted delivery, and NA templated materials. Future perspectives of development are also highlighted.
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Affiliation(s)
- Markéta Paloncýová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Martin Pykal
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Petra Kührová
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Pavel Banáš
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
| | - Jiří Šponer
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- Institute of Biophysics of the Czech Academy of Sciences, v. v. i., Královopolská 135, Brno, 612 65, Czech Republic
| | - Michal Otyepka
- Regional Center of Advanced Technologies and Materials, The Czech Advanced Technology and Research Institute (CATRIN), Palacký University Olomouc, Šlechtitelů 27, Olomouc, 779 00, Czech Republic
- IT4Innovations, VŠB - Technical University of Ostrava, 17. listopadu 2172/15, Ostrava-Poruba, 708 00, Czech Republic
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Côté S, Bouilly D, Mousseau N. The molecular origin of the electrostatic gating of single-molecule field-effect biosensors investigated by molecular dynamics simulations. Phys Chem Chem Phys 2022; 24:4174-4186. [PMID: 35113103 DOI: 10.1039/d1cp04626h] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Field-effect biosensors (bioFETs) offer a novel way to measure the kinetics of biomolecular events such as protein function and DNA hybridization at the single-molecule level on a wide range of time scales. These devices generate an electrical current whose fluctuations are correlated to the kinetics of the biomolecule under study. BioFETs are indeed highly sensitive to changes in the electrostatic potential (ESP) generated by the biomolecule. Here, using all-atom solvent explicit molecular dynamics simulations, we further investigate the molecular origin of the variation of this ESP for two prototypical cases of proteins or nucleic acids attached to a carbon nanotube bioFET: the function of the lysozyme protein and the hybridization of a 10-nt DNA sequence, as previously done experimentally. Our results show that the ESP changes significantly on the surface of the carbon nanotube as the state of these two biomolecules changes. More precisely, the ESP distributions calculated for these molecular states explain well the magnitude of the conductance fluctuations measured experimentally. The dependence of the ESP with salt concentration is found to agree with the reduced conductance fluctuations observed experimentally for the lysozyme, but to differ for the case of DNA, suggesting that other mechanisms might be at play in this case. Furthermore, we show that the carbon nanotube does not impact significantly the structural stability of the lysozyme, corroborating that the kinetic rates measured using bioFETs are similar to those measured by other techniques. For DNA, we find that the structural ensemble of the single-stranded DNA is significantly impacted by the presence of the nanotube, which, combined with the ESP analysis, suggests a stronger DNA-device interplay. Overall, our simulations strengthen the comprehension of the inner working of field-effect biosensors used for single-molecule kinetics measurements on proteins and nucleic acids.
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Affiliation(s)
- Sébastien Côté
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada. .,Département de Physique, Cégep de Saint-Jérôme, Saint-Jérôme, Canada
| | - Delphine Bouilly
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada. .,Institut de recherche en immunologie et cancérologie (IRIC), Université de Montréal, Montréal, Canada.
| | - Normand Mousseau
- Département de Physique, Faculté des Arts et des Sciences, Université de Montréal, Montréal, Canada.
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6
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Fortunati S, Giannetto M, Rozzi A, Corradini R, Careri M. PNA-functionalized magnetic microbeads as substrates for enzyme-labelled voltammetric genoassay for DNA sensing applied to identification of GMO in food. Anal Chim Acta 2021; 1153:338297. [PMID: 33714443 DOI: 10.1016/j.aca.2021.338297] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/21/2022]
Abstract
A novel enzyme-labelled voltammetric magnetogenoassay for DNA sensing based on the use of carboxyl-surface coated magnetic microbeads functionalized with PNA probes and subsequent read-out on screen-printed electrode (SPE) substrates was developed. The assay was validated for determination of non-amplified genomic DNA from genetically modified Roundup Ready soy. Outstanding performance with respect to other genoassays requiring preliminary amplification of target DNA via PCR was demonstrated. The analytical performance was also improved compared to previous methods based on the immobilization of the same PNA probes on SPE substrates, since the method was found capable of achieving LOD and LOQ of 415 fM and 995 fM, respectively. The ability of the magnetogenoassay to detect the presence of Roundup Ready soy DNA sequence was tested on genomic DNA extract from European Reference Material soy flours, demonstrating the capability of the method to match the European Union regulation for labelling of food containing a percentage of GM products greater than 0,9%.
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Affiliation(s)
- Simone Fortunati
- Dipartimento di Scienze Chimiche, Della Vita e Della Sostenibilità Ambientale, Università di Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
| | - Marco Giannetto
- Dipartimento di Scienze Chimiche, Della Vita e Della Sostenibilità Ambientale, Università di Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy.
| | - Andrea Rozzi
- Dipartimento di Scienze Chimiche, Della Vita e Della Sostenibilità Ambientale, Università di Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
| | - Roberto Corradini
- Dipartimento di Scienze Chimiche, Della Vita e Della Sostenibilità Ambientale, Università di Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
| | - Maria Careri
- Dipartimento di Scienze Chimiche, Della Vita e Della Sostenibilità Ambientale, Università di Parma, Parco Area Delle Scienze 17/A, 43124, Parma, Italy
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7
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The transport of Idarubicin therapeutic agent using a novel graphene sheet as a drug delivery platform through a biomembrane. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.115050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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8
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Karachevtsev MV, Stepanian SG, Valeev VA, Lytvyn OS, Adamowicz L, Karachevtsev VA. Adsorption of Polyadenylic acid on graphene oxide: experiments and computer modeling. J Biomol Struct Dyn 2020; 40:425-437. [PMID: 32897172 DOI: 10.1080/07391102.2020.1814869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
In this work, we study the adsorption of poly(rA) on graphene oxide (GO) using AFM and UV absorption spectroscopies. A transformation of the homopolynucleotide structure on the GO surface is observed. It is found that an energetically favorable conformation of poly(rA) on GO is achieved after a considerable amount of time (days). It is revealed that GO can induce formation of self-structures of single-stranded poly(rA) including a duplex at pH 7. The phenomenon is analyzed by polymer melting measurements and observed by AFM. Details of the noncovalent interaction of poly(rA) with graphene are also investigated using molecular dynamics simulations. The adsorption of (rA)10 oligonucleotide on graphene is compared with the graphene adsorption of (rC)10. DFT calculations are used to determine equilibrium structures and the corresponding interaction energies of the adenine-GO complexes with different numbers of the oxygen-containing groups. The IR intensities and vibrational frequencies of free and adsorbed adenines on the GO surface are calculated. The obtained spectral transformations are caused by the interaction of adenine with GO.
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Affiliation(s)
- Maksym V Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Stepan G Stepanian
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Vladimir A Valeev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
| | - Oksana S Lytvyn
- V. Lashkaryov Institute of Semiconductor Physics, National Academy of Sciences of Ukraine Kyiv, Borys Grinchenko Kyiv University, Kyiv, Ukraine
| | - Ludwik Adamowicz
- Department of Chemistry and Biochemistry, University of Arizona, Tucson, AZ, USA.,Interdisciplinary Center for Modern Technologies, Nicolaus Copernicus University, Toruń, PL, Poland
| | - Victor A Karachevtsev
- B. Verkin Institute for Low Temperature Physics and Engineering, National Academy of Sciences of Ukraine, Kharkiv, Ukraine
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Contreras-Torres FF, Basiuk EV, Basiuk VA. A dispersion-corrected density functional theory study of the noncovalent interactions between nucleobases and carbon nanotube models containing stone-wales defects. J Comput Chem 2020; 41:780-789. [PMID: 31837037 DOI: 10.1002/jcc.26127] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2019] [Revised: 09/07/2019] [Accepted: 12/01/2019] [Indexed: 01/08/2023]
Abstract
The noncovalent bonding between nucleobases (NBs) and Stone-Wales (SW) defect-containing closed-end single-walled carbon nanotubes (SWNTs) was theoretically studied in the framework of density function theory using a dispersion-corrected functional PBE-G06/DNP. The models employed in this study were armchair nanotube (ANT) (5,5) and zigzag nanotube (ZNT) (10,0), which incorporated SW defects in different orientations. In one of them, the (7,7) junction is tilted with respect to SWNT axis (ANT-t and ZNT-t), whereas in ANT-p and ZNT-p models the (7,7) junction is parallel and perpendicular to the axis, respectively. The binding energies for uracil, thymine, cytosine, 5-methylcytosine, adenine, and guanine interacting with the defect-containing nanotube models were compared to the values previously obtained with the same calculation technique for the case of defect-free SWNTs, both in the gas phase (vacuum) and in aqueous medium. For most models, the interaction strength tends to be higher for purine than for pyrimidine complexes, with a clear exception of the systems including ZNT-p, both in vacuum and in aqueous medium. As it could be expected, the binding strength in the latter case is lower as compared to that in vacuum, roughly by 2-4 kcal/mol, due to the implicit inclusion of a medium (i.e., water) via the conductor-like screening model model. The closest contacts between NBs and SWNT models, frontier orbital distribution, and highest-occupied molecular orbital-lowest-unoccupied molecular orbital gap energies are analyzed as well. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Elena V Basiuk
- Instituto de Ciencias Aplicadas y Tecnología, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510, Ciudad de México, Mexico
| | - Vladimir A Basiuk
- Instituto de Ciencias Nucleares, Universidad Nacional Autónoma de México, Circuito Exterior C.U., 04510, Ciudad de México, Mexico
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10
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Theoretical study on carbonaceous materials as high efficient carriers for crizotinib drug in liquid water by density functional theory approach. Struct Chem 2020. [DOI: 10.1007/s11224-020-01522-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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11
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Affiliation(s)
- Junwei Yang
- School of Arts and Sciences, Shanghai Dianji University, Shanghai, People’s Republic of China
| | - Yanhong Yuan
- School of Arts and Sciences, Shanghai Dianji University, Shanghai, People’s Republic of China
| | - Guohong Chen
- School of Arts and Sciences, Shanghai Dianji University, Shanghai, People’s Republic of China
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12
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Lata S, Vikas. Concentration dependent adsorption of aromatic organic compounds by SWCNTs: Quantum-mechanical descriptors for nano-toxicological studies of biomolecules and agrochemicals. J Mol Graph Model 2018; 85:232-241. [PMID: 30227368 DOI: 10.1016/j.jmgm.2018.08.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 08/12/2018] [Accepted: 08/20/2018] [Indexed: 12/30/2022]
Abstract
For evaluating the environmental risk associated using carbon nanotubes (CNTs), a successful prediction is desired for the adsorption of organic compounds (OCs) by CNTs at different adsorbate concentrations. This is most often achieved through poly-parameter linear solvation energy relationships (LSERs) based on solvatochromic descriptors. This study examines the real predictivity of the existing LSERs for predicting the adsorption of OCs by single-walled CNTs (SWCNTs) while comparing it with that of the models developed in the present work using quantum-mechanical descriptors. The real predictivity of the quantum-mechanical models and existing LSERs is compared using state-of-the-art statistical procedures employing an external prediction set of compounds not used in the model development. The quantum-mechanically computed mean polarizability, but originating from the interactions between electrons of parallel spin, is found to play an essential role in the adsorption of OCs by SWCNTs. Besides the solvatochromic descriptors (McGowan volume and molar excess refractivity), the instantaneous inter-electronic interactions, captured through electron-correlation based quantum-mechanical descriptors, are found to significantly affect the adsorption at varying adsorbate concentration. The models developed using a combination of quantum-mechanical and solvatochromic descriptors are found to be quite reliable. The models proposed were further employed to predict the adsorption of agrochemicals such as insecticides, pesticides, herbicides, as well as adsorption of endocrine disruptors and biomolecules such as nucleobases and steroid hormones. These are predicted to be strongly adsorbed by SWCNTs with Progesterone and Guanine exhibiting maximal interaction with the SWCNTs among biomolecules. The quantum-mechanical descriptors proposed in this work can be used for the risk assessment of SWCNTs in systems where adsorption is the primary process.
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Affiliation(s)
- Suman Lata
- Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India
| | - Vikas
- Quantum Chemistry Group, Department of Chemistry and Centre of Advanced Studies in Chemistry, Panjab University, Chandigarh, 160014, India.
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Zhuang Q, Cao W, Ni Y, Wang Y. Synthesis-identification integration: One-pot hydrothermal preparation of fluorescent nitrogen-doped carbon nanodots for differentiating nucleobases with the aid of multivariate chemometrics analysis. Talanta 2018; 185:491-498. [DOI: 10.1016/j.talanta.2018.04.019] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 02/10/2018] [Accepted: 04/07/2018] [Indexed: 12/31/2022]
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14
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Karachevtsev V, Stepanian S, Karachevtsev M, Adamowicz L. Graphene induced molecular flattening of meso -5,10,15,20-tetraphenyl porphyrin: DFT calculations and molecular dynamics simulations. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2018.04.009] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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15
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Zarudnev ES, Stepanian SG, Adamowicz L, Leontiev VS, Karachevtsev VA. Comparison of noncovalent interactions of zigzag and armchair carbon nanotubes with heterocyclic and aromatic compounds: Imidazole and benzene, imidazophenazines, and tetracene. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2016.11.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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DNA adsorbed on graphene and graphene oxide: Fundamental interactions, desorption and applications. Curr Opin Colloid Interface Sci 2016. [DOI: 10.1016/j.cocis.2016.09.001] [Citation(s) in RCA: 172] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
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17
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Kosevich MV, Zobnina VG, Stepanian SG, Karachevtsev VA, Adamowicz L. The effect of protonation of cytosine and adenine on their interactions with carbon nanotubes. J Mol Graph Model 2016; 70:77-84. [DOI: 10.1016/j.jmgm.2016.09.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2016] [Revised: 09/08/2016] [Accepted: 09/20/2016] [Indexed: 01/12/2023]
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18
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Ranganathan SV, Halvorsen K, Myers CA, Robertson NM, Yigit MV, Chen AA. Complex Thermodynamic Behavior of Single-Stranded Nucleic Acid Adsorption to Graphene Surfaces. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:6028-34. [PMID: 27219463 DOI: 10.1021/acs.langmuir.6b00456] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
In just over a decade since its discovery, research on graphene has exploded due to a number of potential applications in electronics, materials, and medicine. In its water-soluble form of graphene oxide, the material has shown promise as a biosensor due to its preferential absorption of single-stranded polynucleotides and fluorescence quenching properties. The rational design of these biosensors, however, requires an improved understanding of the binding thermodynamics and ultimately a predictive model of sequence-specific binding. Toward these goals, here we directly measured the binding of nucleosides and oligonucleotides to graphene oxide nanoparticles using isothermal titration calorimetry and used the results to develop molecular models of graphene-nucleic acid interactions. We found individual nucleosides binding KD values lie in the submillimolar range with binding order of rG < rA < rC < dT < rU, while 5mer and 15mer oligonucleotides had markedly higher binding affinities in the range of micromolar and submicromolar KD values, respectively. The molecular models developed here are calibrated to quantitatively reproduce the above-mentioned experimental results. For oligonucleotides, our model predicts complex binding features such as double-stacked bases and a decrease in the fraction of graphene stacked bases with increasing oligonucleotide length until plateauing beyond ∼10-15 nucleotides. These experimental and computational results set the platform for informed design of graphene-based biosensors, further increasing their potential and application.
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Affiliation(s)
- Srivathsan V Ranganathan
- Department of Chemistry and ‡The RNA Institute, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Ken Halvorsen
- Department of Chemistry and ‡The RNA Institute, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Chris A Myers
- Department of Chemistry and ‡The RNA Institute, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Neil M Robertson
- Department of Chemistry and ‡The RNA Institute, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Mehmet V Yigit
- Department of Chemistry and ‡The RNA Institute, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
| | - Alan A Chen
- Department of Chemistry and ‡The RNA Institute, University at Albany, State University of New York , 1400 Washington Avenue, Albany, New York 12222, United States
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19
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Yang J, Yuan Y, Hua Z. Density functional theory study of interaction of graphene with hypoxanthine, xanthine, and uric acid. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1189009] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Junwei Yang
- Department of Mathematics and Physics, Shanghai Dianji University, Shanghai, China
| | - Yanhong Yuan
- Department of Mathematics and Physics, Shanghai Dianji University, Shanghai, China
| | - Zhao Hua
- Department of Mathematics and Physics, Shanghai Dianji University, Shanghai, China
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20
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Ramezanpour M, Leung SSW, Delgado-Magnero KH, Bashe BYM, Thewalt J, Tieleman DP. Computational and experimental approaches for investigating nanoparticle-based drug delivery systems. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2016; 1858:1688-709. [PMID: 26930298 DOI: 10.1016/j.bbamem.2016.02.028] [Citation(s) in RCA: 105] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2016] [Revised: 02/20/2016] [Accepted: 02/23/2016] [Indexed: 12/21/2022]
Abstract
Most therapeutic agents suffer from poor solubility, rapid clearance from the blood stream, a lack of targeting, and often poor translocation ability across cell membranes. Drug/gene delivery systems (DDSs) are capable of overcoming some of these barriers to enhance delivery of drugs to their right place of action, e.g. inside cancer cells. In this review, we focus on nanoparticles as DDSs. Complementary experimental and computational studies have enhanced our understanding of the mechanism of action of nanocarriers and their underlying interactions with drugs, biomembranes and other biological molecules. We review key biophysical aspects of DDSs and discuss how computer modeling can assist in rational design of DDSs with improved and optimized properties. We summarize commonly used experimental techniques for the study of DDSs. Then we review computational studies for several major categories of nanocarriers, including dendrimers and dendrons, polymer-, peptide-, nucleic acid-, lipid-, and carbon-based DDSs, and gold nanoparticles. This article is part of a Special Issue entitled: Membrane Proteins edited by J.C. Gumbart and Sergei Noskov.
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Affiliation(s)
- M Ramezanpour
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - S S W Leung
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - K H Delgado-Magnero
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
| | - B Y M Bashe
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - J Thewalt
- Department of Physics, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - D P Tieleman
- Centre for Molecular Simulation, Department of Biological Sciences, University of Calgary, Calgary, AB T2N 1N4, Canada
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21
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Avramopoulos A, Otero N, Karamanis P, Pouchan C, Papadopoulos MG. A Computational Study of the Interaction and Polarization Effects of Complexes Involving Molecular Graphene and C60 or a Nucleobases. J Phys Chem A 2016; 120:284-98. [PMID: 26690053 DOI: 10.1021/acs.jpca.5b09813] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A systematic analysis of the molecular structure, energetics, electronic (hyper)polarizabilities and their interaction-induced counterparts of C60 with a series of molecular graphene (MG) models, CmHn, where m = 24, 84, 114, 222, 366, 546 and n = 12, 24, 30, 42, 54, 66, was performed. All the reported data were computed by employing density functional theory and a series of basis sets. The main goal of the study is to investigate how alteration of the size of the MG model affects the strength of the interaction, charge rearrangement, and polarization and interaction-induced polarization of the complex, C60-MG. A Hirshfeld-based scheme has been employed in order to provide information on the intrinsic polarizability density representations of the reported complexes. It was found that the interaction energy increases approaching a limit of -26.98 kcal/mol for m = 366 and 546; the polarizability and second hyperpolarizability increase with increasing the size of MG. An opposite trend was observed for the dipole moment. Interestingly, the variation of the first hyperpolarizability is relatively small with m. Since polarizability is a key factor for the stability of molecular graphene with nucleobases (NB), a study of the magnitude of the interaction-induced polarizability of C84H24-NB complexes is also reported, aiming to reveal changes of its magnitude with the type of NB. The binding strength of C84H24-NB complexes is also computed and found to be in agreement with available theoretical and experimental data. The interaction involved in C60 B12N12H24-NB complexes has also been considered, featuring the effect of contamination on the binding strength between MG and NBs.
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Affiliation(s)
- Aggelos Avramopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
| | - Nicolás Otero
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Panaghiotis Karamanis
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Claude Pouchan
- Equipe de Chimie Théorique, ECP Institut des Sciences Analytiques et de Physico-chimie pour l'Environnement et les Matériaux (IPREM) UMR 5254 , Hélioparc Pau Pyrénées 2 avenue du Président Angot, 64053 Pau Cedex 09, Pau, France
| | - Manthos G Papadopoulos
- Institute of Biology, Pharmaceutical Chemistry and Biotechnology, National Hellenic Research Foundation , 48 Vas. Constantinou Avenue, Athens 11635, Greece
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